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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatattcttttagatatacagcaattagactcaaacatcagactgcattttccaagactgacccatatttttgttctcttgtatgttctagGTTATGTTTAGTGTTTCTTACCTTTAGCTGTATTGGCTACGCGATGCCCTTCATCCTCTGTACAACAATATGTTGCTGCTTGCCTTGCATAATCTCAATT

Basic information

species Arabidopsis thaliana
transcript AT4G32600.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G32600.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g54624.1 (Oryza sativa), 3'ss of exon 3
gtgatattcttttagatatacagcaattagactcaaacatcagactgcattttccaagactgacccatatttttgtt-----ctcttgtatgttctagGTTATGTTTAGTGTTTCTTACCTTTAGCTGTATTGGCTACGCGATGCCCTTCATCCTCTGTACAACAATATGTTGCTGCTTGCCTTGCATAATCTCAATT
                           || |  |||| ||     ||  |     ||||    ||| |  | |||||     || || |   | | ||||||||| | ||||| ||||||||||| |||||||| || || ||||| |||||||||||| |||  ||||| |||||| |||| ||||| || ||  ||
--------------------------gtaaatacaaatatttt-ttgtgtggat-aagatgctcccttgatcttgttgctgacttttttccctgccagGTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTTCATCCTCTGTGCAATGATATGCTGCTGCCTGCCCTGCATCATATCTGTT

upper sequence: AT4G32600.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G092244_T03 (Zea mays), 3'ss of exon 3
gtgatattcttttagatatacagcaattagactcaaacatcagactgcattttccaagactgacccatatttttgttctcttgtatgttctagGTTATGTTTAGTGTTTCTTACCTTTAGCTGTATTGGCTACGCGATGCCCTTCATCCTCTGTACAACAATATGTTGCTGCTTGCCTTGCATAATCTCAATT
    |   ||  || |  | |    ||      |  || |  |  | | | || | |   |   | |  | | ||| ||| ||| |  |  ||||| ||  |||  || || || || ||||| |||||||| ||||||||||||||||||||  |    ||||| |||||||| || |||||||||||  | 
---gtgcgctccta-acctgccatgatgg----cgtaccttcgcatacttatttcgatgtt--tcaaggtgtgtgtactcatgttt--ttcagGTTGTGCATAGCCTTCCTCACTTTCAGCTGCATTGGCTATGCGATGCCCTTCATCCTCTGCGCGCTGATATGCTGCTGCTTACCCTGCATAATCTCCCTG

upper sequence: AT4G32600.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G07690.1 (Glycine max), 3'ss of exon 2
----gtgat-attcttttagatatacagcaattagactcaaacatcagactgcattttccaagactgaccca--tatttttgttctcttgtatgttctagGTTATGTTTAGTGTTTCTTACCTTTAGCTGTATTGGCTACGCGATGCCCTTCATCCTCTGTACAACAATATGTTGCTGCTTGCCTTGCATAATCTCAATT
    |  || |||  |  | ||  |    ||  | |  || | || |   |    ||||  |||    ||    ||| | || |  ||| |   |   ||||||||| ||||||||||||| |||||||||||||| || || ||||||||||| || ||| ||||||| || |||||| ||||||||||||| || || 
acaagcaattatttctccaaattaagttgaaccaaatacacaaataatcttctgatttcttagagcttccagattatatctgcttccttttgcttggcagGTTATGTGTAGTGTTTCTTACTTTTAGCTGTATTGGTTATGCTATGCCCTTCATTCTATGTGCAACAATTTGCTGCTGCCTGCCTTGCATAATTTCCATC

upper sequence: AT4G32600.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G07570.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------------------------------------------------gtgatattcttttagatatacag--caattagactcaaacat-----cagactgc--attttccaagactgacccatatt-tttgttctcttgtatgttctagGTTATGTTTAGTGTTTCTTACCTTTAGCTGTATTGGCTACGCGATGCCCTTCATCCTCTGTACAACAATATGTTGCTGCTTGCCTTGCATAATCTCAATT
                                                                                                  |||  |  ||   ||| ||   ||| | ||   ||| |       |  || |  |||||  |   ||  |  || || | || |  ||| |   |   ||||||||| ||||||||||||| |||||||| || || || || ||||||||||| |||||| ||||||| || |||||| ||||||| ||||| || || 
gtatagcctctcagcagctcttacatttagcatgtgtttggtaaaacatttttcaagagaaataatttttcaaaaattctctcatgaagctagcaaaaataaccaattgtttatccaaaccaagttgaacaaaatacacaaataatcttctgattttttagagcttccagattttatctgcttccttttgcttggcagGTTATGTGTAGTGTTTCTTACTTTTAGCTGCATCGGTTATGCTATGCCCTTCATTCTCTGTGCAACAATTTGCTGCTGCCTGCCTTGTATAATTTCCATC

upper sequence: AT4G32600.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G30020.1 (Glycine max), 3'ss of exon 3
gtgatattcttttagatatacagcaattagactcaaacatcagactgcattttccaagactgacccatatttttgttctcttgtatgttctagGTTATGTTTAGTGTTTCTTACCTTTAGCTGTATTGGCTACGCGATGCCCTTCATCCTCTGTACAACAATATGTTGCTGCTTGCCTTGCATAATCTCAATT
    ||  |||| |   || |     ||  | | || | ||||| |  |   |  |  |   |   |||| |   |  | |    ||    ||||||||| ||||||||||| | |||||||| ||||| || || ||||||||||| |||||| ||||||| || || ||  | ||||| ||||| || || 
---gtagcctttcattcattc-----ttgcatttaatcttcagattttaagat--attatgaaattatatctgcttcatatctcttggc--agGTTATGTATAGTGTTTCTTGCATTTAGCTGCATTGGTTATGCCATGCCCTTCATTCTCTGTTCAACAATCTGCTGTTGTCTCCCTTGTATAATTTCTATC

upper sequence: AT4G32600.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0008g04280.t01 (Vitis vinifera), 3'ss of exon 3
gtgatattcttttagatatacagcaattagactcaaacatcagactgcattttccaagactgacccatatttttgttctcttgtatgttctagGTTATGTTTAGTGTTTCTTACCTTTAGCTGTATTGGCTACGCGATGCCCTTCATCCTCTGTACAACAATATGTTGCTGCTTGCCTTGCATAATCTCAATT
||  | ||   |   || ||   || || | |     ||| |  || | || |   |||   || ||   | || ||  | | |       ||||||||| |||| |||||||||||||||||||| || || || ||||| ||||| || ||| | ||||| || |||||| | ||||| ||||| || || 
gtattgtttagtaccatttatcacattttgtcatttccatta--ctcccttctgtgaga---actcaacctattctttgcatttcctcatcagGTTATGTATAGTCTTTCTTACCTTTAGCTGTATCGGATATGCCATGCCGTTCATTCTATGTGCTACAATCTGCTGCTGCCTCCCTTGTATAATTTCCATC

upper sequence: AT4G32600.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ27808 (Selaginella moellendorffii), 3'ss of exon 2
gtgatattcttttagatatacagcaattagactcaaacatcagactgcattttccaagactgacccatatttttgttctcttgtatgttctagGTTATGTTTAGTGTTTCTTACCTTTAGCTGTATTGGCTACGCGATGCCCTTCATCCTCTGTACAACAATATGTTGCTGCTTGCCTTGCATAATCTCAATT
                                    | | || | |||  | |    |  || | |||  ||||  | || ||| | | | ||||| ||| | || || ||||| |||||||| ||||| ||||| |||||||| || || ||  | || ||||||||||||||||| ||||||||| || | 
------------------------------gtatggaga-cacattgcgctctgtttg--tgcctcatcatttttgtttcctgtttctgc-agGTTGTGTATTGTTTTCCTTACTTTTAGCTGCATTGGATACGCCATGCCCTTTATTCTGTGCGCGACTATATGTTGCTGCTTGCCGTGCATAATCGCACTG

upper sequence: AT4G32600.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ36853 (Selaginella moellendorffii), 3'ss of exon 2
gtgatattcttttagatatacagcaattagactcaaacatcagactgcattttccaagactgacccatatttttgttctcttgtatgttctagGTTATGTTTAGTGTTTCTTACCTTTAGCTGTATTGGCTACGCGATGCCCTTCATCCTCTGTACAACAATATGTTGCTGCTTGCCTTGCATAATCTCAATT
                                    | | || | |||  ||| |  |  || | |||  ||||  | || ||| |   | ||||| ||| | || || ||||| |||||||| ||||| ||||| |||||||| || || ||  | || ||||||||||||||||| ||||||||| || | 
------------------------------gtatggaga-cacattgcgctttgcttg--tgcctcatcatttttgtttcctgtttcggc-agGTTGTGTATTGTTTTCCTTACTTTTAGCTGCATTGGATACGCCATGCCCTTTATTCTGTGCGCGACTATATGTTGCTGCTTGCCGTGCATAATCGCACTG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|86073538|gb|DR369295.1|DR369295
EST:     TGGATATTTGGAGGGCATTCATCTGCTGCCGAGGCTCCTAACTTGTACAG                         GTTATGTTTAGTGTTTCTTACCTTTAGC
genomic: TGGATATTTGGAGGGCATTCATCTGCTGCCGAGGCTCCTAACTTGTACAGgtgatattct ... tatgttctagGTTATGTTTAGTGTTTCTTACCTTTAGC
EST: gi|124819470|gb|EH904336.1|EH904336
EST:     TGGATATTTGGAGGGCATTCATCTGCTGCCGAGGCTCCTAACTTGTACAG                         GTTATGTTTAG
genomic: TGGATATTTGGAGGGCATTCATCTGCTGCCGAGGCTCCTAACTTGTACAGgtgatattct ... tatgttctagGTTATGTTTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcagactgcattttccaagactgacccatatttttgttctcttgtatgttctagGTTATGTTTAGTGTTTCTTACCTTTAGCTGTATTGGCTACGCGATGCCCTTCATCCTCTGTACAACAATATGTTGCTGCTTGCCTTGCATAATCTCAATT
                   gactgac  putative branch site (score: 2)
                               tttttgttctcttgt  putative PPT
                            atatttttgtt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatattcttttagatatacagcaattagactcaaacatcagactgcattttccaagactgacccatatttttgttctcttgtatgttctagGTTATGTTTAGTGTTTCTTACCTTTAGCTGTATTGGCTACGCGATGCCCTTCATCCTCTGTACAACAATATGTTGCTGCTTGCCTTGCATAATCTCAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT